Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I have an error: niiRead(): error opening file /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi2.flt.nii.gzWARN: Could not open /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS.flt.trk for readingWARN: Error was: Can not open fileWARN: Skipping to next subject dmri_train(5801) malloc: *** mmap(size=159744) failed (error code=12)*** error: can't allocate region*** set a breakpoint in malloc_error_break to debugMRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice Cannot allocate memoryDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 What's meaning?
Stefano
----Messaggio originale---- Da: shantanu@nmr.mgh.harvard.edu Data: 5-feb-2013 21.53 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu, ayendiki@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: tracula and recon-all
Hi Stefano,
Just use the cp command to move your recon-all directories to the Diff01 directory and source it from there.
HTH, Shantanu
On Tue, February 5, 2013 3:38 pm, stdp82@virgilio.it wrote:
Because initially I have run recon-all and trac-all in two separate folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and data.nii.gz in Diff01 When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id I do not understand as I should placed the my file in the folder.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-feb-2013 21.08 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: tracula and recon-all
Why do you want to rerun recon-all after trac-all? You just need to run it before trac-all.
On Tue, 5 Feb 2013, stdp82@virgilio.it wrote:
No, I 'm sorry. I try to reformulate my question. I have a folder called Diff01 in my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova) This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt, bvals.txt and MPRAGE.nii.gz.
Which is the exact command line (and the exact files name in the folder) that you advise me for running recon-all and after trac-all?
Stefano
You mean the exact command line to delete a folder? It's rm -rf.
On Tue, 5 Feb 2013, stdp82@virgilio.it wrote:
Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
have
data.nii.gz bvecs bvals MPRAGE.nii.gz
If I write on terminal
recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject $SUBJECTS_DIR/Diff01
with this ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should
delete
the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then
How is the exact command line, please?
Thanks,
Stefano
omit all -i flags.The subject name needs to be the same for recon-all
and t
rac-all. There is no way for trac-all to guess that hpth_subj01 and Diff01 are the same subject.
Hi Anastasia, my original folder Diff01 in /Applications/freesurfer/subjects/subject_prova/Diff01 now contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
runned
recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject but I still have this error: /Applications/freesurfer/bin/dmri_train --outdir /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
--out
lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
lh.ilf_AS_avg33_mni_flt
rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
rh.unc_AS_avg33_mni_flt
fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
lh.atr_PP_avg33_mni_flt
rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
rh.cab_PP_avg33_mni_flt
lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
lh.slfp_PP_avg33_mni_flt
rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
rh.slft_PP_avg33_mni_flt
--slist /tmp/subj33.Diff01.21529.txt --trk
dlabel/mni/lh.cst_AS.flt.trk
dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
--cmask
dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0
0 0 0
0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
dlabel/mni/fmajor_PP_roi1.flt.nii.gz
dlabel/mni/fmajor_PP_roi2.flt.nii.gz
dlabel/mni/fminor_PP_roi1.flt.nii.gz
dlabel/mni/fminor_PP_roi2.flt.nii.gz
dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
/Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
in_mask.flt.nii.gz
--fa
/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
flt.nii.gz
--ncpts 5 --debugERROR: fio_pushd: /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: must specify brain mask volume for output subjectDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct
18
12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Feb 5 07:54:09 CET 2013 Why? Can it depends from the files in the original folder Diff01?
Please,
if yes, may you explain which is the better arrangement of the
MPRAGE and
DWI in the folders. Thank you very much,
Stefano
----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 4-feb-2013 4.48 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: tracula bvecs error
No, putting your T1 in a folder is not the same as running
freesurfer on
it. You need to run recon-all on your T1. This is a piece of
software that
will segment your T1 (among other things). Tracula will need that segmentation to reconstruct your tracts.
On Sun, 3 Feb 2013, std...@virgilio.it wrote:
Hi Anastasia, I have put T1 in
/Applications/freesurfer/subjects/subject_prova/Diff01/
together data.nii.gz, bvals and bvecs. My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_prova T1 was called as T1_01.nii.gz. This is well done?
Thanks,
Stefano
----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 3-feb-2013 20.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] tracula bvecs error
Do you have a freesurfer recon of your subject's T1 in the $SUBJECTS_DIR?
On Sun, 3 Feb 2013, std...@virgilio.it wrote:
I think that I have resolved the bvecs error by using sudo nano
option
but
now in the next step I visualize this error: ERROR: fio_pushd: /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni ERROR: must specify brain mask volume for output subject
Thanks,
Stefano
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